General information for g3384.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S acidic ribosomal protein P0.
Parent gene
- The parent gene g3384 is located on chr_3: 25010458..25011604 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g3384 | g3384.t3 | isoform | g3384.t3 | 25007360 | 25011330 |
| chr_3 | g3384 | g3384.t3 | exon | g3384.t3.exon1 | 25007360 | 25007595 |
| chr_3 | g3384 | g3384.t3 | exon | g3384.t3.exon2 | 25009830 | 25010140 |
| chr_3 | g3384 | g3384.t3 | cds | g3384.t3.CDS1 | 25010043 | 25010140 |
| chr_3 | g3384 | g3384.t3 | exon | g3384.t3.exon3 | 25010203 | 25011001 |
| chr_3 | g3384 | g3384.t3 | cds | g3384.t3.CDS2 | 25010203 | 25011001 |
| chr_3 | g3384 | g3384.t3 | exon | g3384.t3.exon4 | 25011277 | 25011330 |
| chr_3 | g3384 | g3384.t3 | cds | g3384.t3.CDS3 | 25011277 | 25011330 |
| chr_3 | g3384 | g3384.t3 | TSS | g3384.t3 | 25011604 | 25011604 |
| chr_3 | g3384 | g3384.t3 | TTS | g3384.t3 | NA | NA |
Sequences
>g3384.t3 Gene=g3384 Length=1400
ATGGTTAGGGAGAACAAGGCCACCTGGAAAGCTAACTACTTCTTAAAAGTCGTGACATAT
CTCGACGAATATCCAAAATGTTTCATCGTCGGTGCCGATAACGTTGGTTCAAAGCAAATG
CAGCAAATTCGTATCTCACTTCGTGGACTCGCTGTAGTCTTGATGGGCAAGAACACTATG
ATGCGTAAAGCCATTAAGGGCCATTTGGAAAACAATCAAGCCCTCGACAGAATTTTACCA
CACATTCGTGGTAATGTTGGTTTCGTTTTCACAAAGGGAGATTTGAATGAAGTTCGCGAA
AAGTTGTTGCAAAACAAAGTTCGTGCTCCTGCTCGTGCTGGCGCAATTGCTCCTTGTGAA
GTAATTATTCCTGCTCAAAATACTGGTTTGGGTCCAGAAAAAACAAGTTTCTTCCAAGCT
CTTTCAATTCCAACAAAGATTTCAAAGGGTACTATTGAAATTATCAATGATGTGCCCATC
TTAAAGCCTGGTGACAAAGTCGGTGCTTCTGAAGCTACTTTGCTCAACATGTTGAACATC
TCTCCATTCTCATATGGTTTGGTAATTGAGCAAGTTTATGATTCAGGAAGCATCTTCTCT
CCAAATATCTTGGACATCAAACCAGAAGATTTGCGTGCTAAATTCCAACAAGGAGTTGCA
AACGTTGCCGCTCTTTCATTGGCTATGGGCTATCCAACAATTGCCTCTGCTCCACATTCA
ATTGCCAATGGTTTCAAGAACTTGCTCGCTATCGCAGCTGTTACCGATGTCGAATTCAAG
CAGGCTGAAACTGTTAAAGAATTCCTTAAGGATCCATCTAAGTTTGCCGCTGCTGCTGCT
GCATCAGCTCCAGCTGCTTCTGCCGCTGCACCAGCTGCTAAAGCTGAAGCCAAGAAAGAA
GAGTCAGAACCAGAGTCTGATGACGACATGGGATTCGGACTTTTTGATTAAACATTGCAA
CATCATCAAATGGTCATTACAATTTGAATCAACGTTAATTTTCTTCTGCAATAAATTTGC
AAATACTTGCCCATCAATGGCAACTTGCAATTTTTATTGCAAAATAAAGAATTGATTCTT
TTCACACCATTACATCATTTAAATTGTGTTTTTGCCTGAAGACCGGCAATTTAATGCTGA
AATAAAATTGACCAAAAAAAAACAAAATTCAGAATTCCCATTTGAATAAAATTCGTTTTG
AAAAAAGACCTATGTATGTACATCATGCTCTATACACACATTTTCAGAAAATCCAAACCC
AACATCGAATGAAGAGCGAATATATGGGGAAAGTGCTTCATTCTCTTTCTCCCTATATTT
TAATGGGGTTGAAATAGATACAAAATGATTAATTCACTTTGTCCATTAAATTTTAGTTTA
TTTTAATCATCATGAATCTC
>g3384.t3 Gene=g3384 Length=316
MVRENKATWKANYFLKVVTYLDEYPKCFIVGADNVGSKQMQQIRISLRGLAVVLMGKNTM
MRKAIKGHLENNQALDRILPHIRGNVGFVFTKGDLNEVREKLLQNKVRAPARAGAIAPCE
VIIPAQNTGLGPEKTSFFQALSIPTKISKGTIEIINDVPILKPGDKVGASEATLLNMLNI
SPFSYGLVIEQVYDSGSIFSPNILDIKPEDLRAKFQQGVANVAALSLAMGYPTIASAPHS
IANGFKNLLAIAAVTDVEFKQAETVKEFLKDPSKFAAAAAASAPAASAAAPAAKAEAKKE
ESEPESDDDMGFGLFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3384.t3 | CDD | cd05795 | Ribosomal_P0_L10e | 9 | 182 | 3.16915E-101 |
| 8 | g3384.t3 | Gene3D | G3DSA:3.90.105.20 | - | 110 | 182 | 4.0E-32 |
| 7 | g3384.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 284 | 316 | - |
| 4 | g3384.t3 | PANTHER | PTHR45699 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 316 | 3.2E-149 |
| 5 | g3384.t3 | PANTHER | PTHR45699:SF3 | 60S ACIDIC RIBOSOMAL PROTEIN P0 | 1 | 316 | 3.2E-149 |
| 9 | g3384.t3 | PIRSF | PIRSF039087 | L10E | 1 | 316 | 3.0E-140 |
| 2 | g3384.t3 | Pfam | PF00466 | Ribosomal protein L10 | 7 | 104 | 1.7E-19 |
| 1 | g3384.t3 | Pfam | PF17777 | Insertion domain in 60S ribosomal protein L10P | 111 | 180 | 5.5E-22 |
| 3 | g3384.t3 | Pfam | PF00428 | 60s Acidic ribosomal protein | 231 | 315 | 1.7E-18 |
| 6 | g3384.t3 | SUPERFAMILY | SSF160369 | Ribosomal protein L10-like | 8 | 132 | 9.94E-17 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042254 | ribosome biogenesis | BP |
KEGG
Orthology
- This transcript has been annotated with K02941 (large subunit ribosomal protein LP0)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
